Taxonomy analysis on SRA submission inconsistent

[plbergsa]

Case Information: Case #: CAS-1078261-J6B3G5 Customer Name: Bergsagel, Leif, M.D. Customer Email: [email protected] Case Created: 3/12/2023, 3:33:05 AM

Summary: PRJNA938752

Details: I have had a problem with Taxonomy analysis of murine samples I have submitted to SRA. I submitted multiple RNAseq, wxs and low pass mate-pair WGS aligned to GRCm39, which were all correctly identified as mus musculus. However, all of the regular WGS files were not identified as mus musculus, with no predominant organisms Identified. Independently I discovered that one of the samples (SRR23619415) contained a sequence from human chrY, and in fact the taxonomy analysis correctly identified 0.32% homo sapiens in that sample, but did not identify the predominant mus musculus sequences. Can you help correct this?

Wgs https://dataview.ncbi.nlm.nih.gov/object/SRR23619373 0.08% mus caroli wgs https://dataview.ncbi.nlm.nih.gov/object/SRR23619415 0.32% homo sapiens

mate-pair https://dataview.ncbi.nlm.nih.gov/object/SRR23619250 70.62% mus musculus wxs https://dataview.ncbi.nlm.nih.gov/object/SRR23619426 71.95% mus musculus RNAseq https://dataview.ncbi.nlm.nih.gov/object/SRR23619404 55.01% mus musculus

Response from NLM From: NLM Support [email protected] Date: Tuesday, March 14, 2023 at 9:46 AM To: Bergsagel, Leif, M.D. [email protected] Subject: [EXTERNAL] Re: case #CAS-1078261-J6B3G5: PRJNA938752 TRACKING:000414000018578 We cannot fix taxonomy analysis produced by software. Perhaps you sample was contaminated?